AssertionError: ID tag is required for a Display Application
Dear Galaxy Team, I am trying to create my own visualization for a unique datatype but I cannot get past this error in the load. Where is the ID tag assigned for my visualization? Thanks Bob galaxy.datatypes.registry ERROR 2015-12-10 15:10:13,440 Error loading display application (/home/HM_galaxy/config/plugins/visualizations/heatmap/config/heatmap.xml): ID tag is required for a Display ApplicationTraceback (most recent call last): File "/home/HM_galaxy/lib/galaxy/datatypes/registry.py", line 563, in load_display_applications display_app = DisplayApplication.from_file( config_path, app ) File "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py", line 253, in from_file return cls.from_elem( parse_xml( filename ).getroot(), app, filename=filename ) File "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py", line 257, in from_elem att_dict = cls._get_attributes_from_elem( elem ) File "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py", line 265, in _get_attributes_from_elem assert display_id, “ID tag is required for a Display Application”AssertionError: ID tag is required for a Display Application The /visualizations/heatmap/config/heatmap.xml file it is complaining about is below and I have a template under /templates <?xml version="1.0" encoding="UTF-8" ?><!DOCTYPE visualization SYSTEM "../../visualization.dtd"><visualization name="heatmap"> <data_sources> <data_source> <model_class>HistoryDatasetAssociation</model_class> <test type="isinstance" test_attr="datatype" result_type="datatype">text.chm</test> <to_param param_attr="id">dataset_id</to_param> </data_source> </data_sources> <params> <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> </params> <template>heatmap.mako</template></visualization>
Despite sounding very similar, visualizations and display applications are different things - display applications for the most part send or expose Galaxy data to outside sources, visualizations run on the Galaxy server and the client side. It seems like you are trying to configure a visualization as a display application. I would figure out which you need and base your example plugin on an existing type of that. More information @ https://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications... https://wiki.galaxyproject.org/Learn/Visualization -John On Thu, Dec 10, 2015 at 9:32 PM, <rbrown1422@comcast.net> wrote:
Dear Galaxy Team, I am trying to create my own visualization for a unique datatype but I cannot get past this error in the load. Where is the ID tag assigned for my visualization? Thanks Bob
galaxy.datatypes.registry ERROR 2015-12-10 15:10:13,440 Error loading display application (/home/HM_galaxy/config/plugins/visualizations/heatmap/config/heatmap.xml): ID tag is required for a Display Application Traceback (most recent call last): File "/home/HM_galaxy/lib/galaxy/datatypes/registry.py", line 563, in load_display_applications display_app = DisplayApplication.from_file( config_path, app ) File "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py", line 253, in from_file return cls.from_elem( parse_xml( filename ).getroot(), app, filename=filename ) File "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py", line 257, in from_elem att_dict = cls._get_attributes_from_elem( elem ) File "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py", line 265, in _get_attributes_from_elem assert display_id, “ID tag is required for a Display Application” AssertionError: ID tag is required for a Display Application
The /visualizations/heatmap/config/heatmap.xml file it is complaining about is below and I have a template under /templates
<?xml version="1.0" encoding="UTF-8" ?> <!DOCTYPE visualization SYSTEM "../../visualization.dtd"> <visualization name="heatmap"> <data_sources> <data_source> <model_class>HistoryDatasetAssociation</model_class> <test type="isinstance" test_attr="datatype" result_type="datatype">text.chm</test> <to_param param_attr="id">dataset_id</to_param> </data_source> </data_sources> <params> <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> </params> <template>heatmap.mako</template> </visualization>
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Jack, Yes I want to view internal to Galaxy's middle pane like the eyeball does. Do data both visualization and display applications use the icon at the bottom left of the History? So with display applications one does not need an ID tag? Thanks Bob ----- Original Message -----From: John Chilton <jmchilton@gmail.com>To: rbrown1422@comcast.netCc: galaxy-dev <galaxy-dev@lists.galaxyproject.org>Sent: Thu, 10 Dec 2015 22:31:32 -0000 (UTC)Subject: Re: [galaxy-dev] AssertionError: ID tag is required for a Display Application Despite sounding very similar, visualizations and display applicationsare different things - display applications for the most part send orexpose Galaxy data to outside sources, visualizations run on theGalaxy server and the client side. It seems like you are trying to configure a visualization as a displayapplication. I would figure out which you need and base your exampleplugin on an existing type of that. More information @ https://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications... -John On Thu, Dec 10, 2015 at 9:32 PM, <rbrown1422@comcast.net> wrote:> Dear Galaxy Team,> I am trying to create my own visualization for a unique datatype but I> cannot get past this error in the load. Where is the ID tag assigned for my> visualization?> Thanks> Bob>> galaxy.datatypes.registry ERROR 2015-12-10 15:10:13,440 Error loading> display application> (/home/HM_galaxy/config/plugins/visualizations/heatmap/config/heatmap.xml):> ID tag is required for a Display Application> Traceback (most recent call last):> File "/home/HM_galaxy/lib/galaxy/datatypes/registry.py", line 563, in> load_display_applications> display_app = DisplayApplication.from_file( config_path, app )> File> "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py",> line 253, in from_file> return cls.from_elem( parse_xml( filename ).getroot(), app,> filename=filename )> File> "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py",> line 257, in from_elem> att_dict = cls._get_attributes_from_elem( elem )> File> "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py",> line 265, in _get_attributes_from_elem> assert display_id, “ID tag is required for a Display Application”> AssertionError: ID tag is required for a Display Application>> The /visualizations/heatmap/config/heatmap.xml file it is complaining> about is below and I have a template under /templates>> <?xml version="1.0" encoding="UTF-8" ?>> <!DOCTYPE visualization SYSTEM "../../visualization.dtd">> <visualization name="heatmap">> <data_sources>> <data_source>> <model_class>HistoryDatasetAssociation</model_class>> <test type="isinstance" test_attr="datatype"> result_type="datatype">text.chm</test>> <to_param param_attr="id">dataset_id</to_param>> </data_source>> </data_sources>> <params>> <param type="dataset" var_name_in_template="hda"> required="true">dataset_id</param>> </params>> <template>heatmap.mako</template>> </visualization>>>> ___________________________________________________________> Please keep all replies on the list by using "reply all"> in your mail client. To manage your subscriptions to this> and other Galaxy lists, please use the interface at:> https://lists.galaxyproject.org/>> To search Galaxy mailing lists use the unified search at:> http://galaxyproject.org/search/mailinglists/
participants (2)
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John Chilton
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rbrown1422@comcast.net